def get_resource_history(col, resource):
uid = doc_or_uid_to_uid(resource)
cursor = col.find({'resource': uid})
for doc in cursor:
for k in ['new', 'old']:
d = doc[k]
d.pop('_id', None)
d['id'] = d['uid']
doc[k] = Document('resource', d)
doc.pop('_id', None)
yield Document('update', doc)
def _find_local(fname, qparams, as_doct=False):
"""Find a document created using the local framework
Parameters
-----------
fname: str
Name of the query should be run
qparams: dict
Query parameters. Similar to online query methods
Yields
------------
c: doct.Document, StopIteration
Result of the query if found
"""
res_list = []
try:
with open(fname, 'r') as fp:
local_payload = ujson.load(fp)
qobj = mongoquery.Query(qparams)
for i in local_payload:
if qobj.match(i):
res_list.append(i)
except FileNotFoundError:
raise RuntimeWarning('Local file {} does not exist'.format(fname))
if as_doct:
for c in res_list:
yield Document(fname.split('.')[0], c)
else:
for c in res_list:
yield c
def find(self, as_document=False, **kwargs):
"""Given a set of mongo search parameters, return a requests iterator
Parameters
-----------
as_document: bool
Format return type to doct.Document if set
Yields
----------
dict, doct.Document
Result of the query
Raises
---------
StopIteration, requests.exceptions.HTTPError
When nothing found or something is wrong on the server side. If server error occurs,
a human friendly message is returned.
"""
content = _get(self._req_url, kwargs)
if as_document:
for c in content:
yield Document('Request', c)
else:
for c in content:
yield c
def test_find_sample_as_doc():
m_sample = dict(name='comp_sam', uid=str(uuid.uuid4()),
time=ttime.time(), owner='arkilic', project='trial',
beamline_id='trial_b', container='legion1')
s1 = SampleReference(host=TESTING_CONFIG['host'],
port=TESTING_CONFIG['port'])
s1.create(**m_sample)
s_ret = next(s1.find(uid=m_sample['uid'], as_document=True))
assert s_ret == Document('Sample', m_sample)
def find(self, as_document=False, **kwargs):
"""Given a set of MongoDB search parameters, return a requests iterator"""
content = _get(self._cont_url, kwargs)
if as_document:
for c in content:
yield Document('container', c)
else:
for c in content:
yield c
def get_document(url, doc_type, as_json, contents):
r = requests.get(url, params=ujson.dumps(contents))
r.raise_for_status()
content = ujson.loads(r.text)
if as_json:
return r.text
else:
for c in content:
yield Document(doc_type, c)
def test_configuration_find(config_ref):
config_data = dict(beamline_id='test_bl',
uid=str(uuid.uuid4()),
active=True,
time=ttime.time(),
key='test_config',
params=dict(param1='test1', param2='test2'))
config_ref.create(**config_data)
c_ret = next(config_ref.find(uid=config_data['uid'], as_document=True))
assert c_ret == Document('Configuration', config_data)
def test_find_sample_as_doc(conn=conn):
m_sample = dict(name='comp_sam',
uid=str(uuid.uuid4()),
time=ttime.time(),
owner='arkilic',
project='trial',
beamline_id='trial_b',
container='legion1')
conn.create_sample(**m_sample)
s_ret = conn.find_sample(uid=m_sample['uid'], as_document=True)
assert s_ret[0] == Document('Sample', m_sample)
def insert_resource(col, spec, resource_path, resource_kwargs, known_spec,
root):
resource_kwargs = dict(resource_kwargs)
if spec in known_spec:
js_validate(resource_kwargs, known_spec[spec]['resource'])
resource_object = dict(spec=str(spec),
resource_path=str(resource_path),
root=str(root),
resource_kwargs=resource_kwargs,
uid=str(uuid.uuid4()))
col.insert_one(resource_object)
# maintain back compatibility
resource_object['id'] = resource_object['uid']
resource_object.pop('_id', None)
return Document('resource', resource_object)
def find(self, as_document=False, **kwargs):
"""
Parameters
----------
as_document: bool
Formats output to doct.Document if True
Yields
------
c : dict, doct.Document
Documents which have all keys with the given values
"""
content = _get(self._samp_url, params=kwargs)
if as_document:
for c in content:
yield Document('Sample', c)
else:
for c in content:
yield c
def insert_datum(col, resource, datum_id, datum_kwargs, known_spec,
resource_col):
try:
resource['spec']
except (AttributeError, TypeError):
resource = resource_col.find_one({'uid': resource})
spec = resource['spec']
if spec in known_spec:
js_validate(datum_kwargs, known_spec[spec]['datum'])
datum = dict(resource=resource['uid'],
datum_id=str(datum_id),
datum_kwargs=dict(datum_kwargs))
col.insert_one(datum)
# do not leak mongo objectID
datum.pop('_id', None)
return Document('datum', datum)
def find(self, as_document=False, active_only=True, **kwargs):
"""
Parameters
----------
as_document: bool
Formats output to doct.Document if True
active_only: bool
Retrieve only active configurations. Default is True
Yields
------
c: dict, doct.Document
Documents which have all keys with the given values
"""
kwargs['active_only'] = active_only
content = _get(self._conf_url, params=kwargs)
if as_document:
for c in content:
yield Document('Configuration', c)
else:
for c in content:
yield c
def resource_given_uid(col, resource):
uid = doc_or_uid_to_uid(resource)
ret = col.find_one({'uid': uid})
ret.pop('_id', None)
ret['id'] = ret['uid']
return Document('resource', ret)